News

Jun192017

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.1 release. This is a bugfix release, with minor changes in functionality. The following fixes are in this release:

NEW: Family records

Extensive improvements in the pedigree editor now enable physicians to create, follow and update multiple patients within one family in one place. All family members share a single pedigree, accessible either from the patient record or from the newly added Family record.

Almost all of the patient data changes in the pedigree editor will now be reflected on the corresponding patient record and vice versa. An entire family can be constructed within the pedigree editor: existing PhenoTips patient records can be linked to (and unlinked from) individuals in the pedigree, and new patient records can be created as well.

The existing access rights functionality enables different physicians to share access to their patients, so one family can contain a collection of patients that are cared for by different clinicians or scientists. The access level for each individual patient is defined in the patient record by their caring physician.

All families that a user can access are now available for browsing on the homepage, as well as on the newly added Families Directory page.

The old way of entering family studies through explicitly linking patient records is now disabled. The data that was previously entered is preserved and can be viewed in read only mode once an administrator enables the visibility of it. Existing families will be automatically migrated. The automated migration may not be possible for families with ambiguous relationships or for patients cared for by different physicians (the latter is to preserve patient privacy). Those families will require manual adjustments in the pedigree editor.

Patient record improvements

Added "Life status" field in the patient form to allow more logical workflow when entering patient data

Added support for recording twin number (A/B/Other) for patients from a multiple gestation

Embryonal and Fetal onsets are now options under the newly added "Antenatal onset" category in Global age of onset and the phenotype modifiers

The list of subcategories (if they exist) is automatically expanded upon selecting YES for a phenotype

Pressing Enter now selects the first phenotype suggestion from the drop-down

OMIM diagnosis suggestions are now shown in view mode too

Improved support for recording genes and variants

PhenoTips is now storing genes by using Ensembl IDs internally instead of using gene symbols

The new Gene panels section, that can be enabled in the Administration, displays suggested genes based on the phenotypes describing the patient. Similarly to the OMIM suggestions, this section offers an interactive interface allowing to select which phenotypes to ignore when looking for matching genes. The phenotype-to-gene annotations that enable these gene suggestions are provided by the HPO team and are available for download on their website.

Working clinical diagnosis was added to the Diagnosis section

Global mode of inheritance and global age of onset are taken into account when determining suggestions for diagnosis and other phenotypes to investigate

When navigating away from a record, a warning is shown if there are unsaved changes

It is now possible to filter patient records by candidate gene and working clinical diagnosis

NEW: Patient consents

Support for configuring and recording consents obtained from the patient has been added. Consents can be either passive, allowing the simple recording of the consents the patient has granted, or they can be active, affecting what information can be entered. Consents marked as mandatory prevent any data from being recorded until they are checked. Alternatively, a consent can restrict only certain fields from the patient record.

Pedigree editor improvements

Improved pedigree load time

The pedigree image service now supports downloading the file instead of just displaying it

Pedigrees can be exported as PNG/SVG directly from the patient record and from the pedigree export dialog

Improved pedigree JSON export and import

Pedigree editor now allows any node to have any gender

The order of the proband parents is enforced to be father-left mother-right

NEW: Multiple language support

PhenoTips now supports multiple languages and can be configured to work either in single or multi-language mode, by setting multilingual option in the administration's localization page. Single language mode operates in the language chosen as the default in the administration's localization page.

Packaging

The Mac OS X .dmg package should now start when only the JRE is installed (previously it sometimes failed when JDK 1.6 was installed, but only the JRE for 1.7 or 1.8).

When installed on Windows, PhenoTips data is now stored under the current user's home directory by default, allowing installation under Program Files and easier upgrades.

User self-registration is disabled by default, an administrator must either re-enable self-registration or create user accounts.

Other changes

URLs are shorter, as bin/ has been removed by default.

Starting with this version, each PhenoTips installation sends anonymous general installation and usage metadata to a central server located at https://stats.phenotips.org/. The information consists of:

Technical data, such as OS, java version and vendor, servlet container, database used, PhenoTips version, enabled extensions, which help us focus our efforts on the most popular configurations and know when it's a good time to switch to a new version or drop compatibilities without affecting our users

Generic usage metadata: number of users, number of patient records, which will be used, in an aggregated form, in grant applications to receive funding that allows us to continue developing PhenoTips as free software.

PhenoTips installations running in closed networks without access to the internet will not be able to send any data to our stats server. This does not affect in any way the functioning of the software.

Mar222017

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3 Release Candidate 3. The following fixes and improvements are in this release:

Defects

PT-1688 - Check box and delete icon are both visible in OMIM diagnosis field.PT-3151 - Upgrading the RPM installation does not add the ORPHANET indexPT-3154 - Incorrect text in OMIM disorder field description - "i" buttonPT-3158 - "phenotips.IndexOntology.version" displayed in place of the actual version in vocabulary term descriptions